yield batch
def worker(input):
output = input.split(".",-1)[0] + '.extracted.fa'
with open(output, 'w') as o:
with open(input, 'rU') as i:
SeqRecords = SeqIO.parse(i, 'fasta')
SeqIO.write(stripPrimer(SeqRecords), o, 'fasta')
#remove logfile if exists
log_name = args.out + '.log'
if os.path.isfile(log_name):
os.remove(log_name)
ufitslib.setupLogging(log_name)
FNULL = open(os.devnull, 'w')
cmd_args = " ".join(sys.argv)+'\n'
ufitslib.log.debug(cmd_args)
print "-------------------------------------------------------"
FileName = args.fasta
fwdLen = len(FwdPrimer)
if not args.trimming:
ufitslib.log.info("Searching for primers, this may take awhile: Fwd: %s Rev: %s" % (args.F_primer, args.R_primer))
else:
ufitslib.log.info("Working on file: %s" % FileName)
if not args.cpus:
cpus = multiprocessing.cpu_count()
action='store_true',
help='Remove Intermediate Files')
args = parser.parse_args()
def checkfastqsize(input):
filesize = os.path.getsize(input)
return filesize
#remove logfile if exists
log_name = args.out + '.ufits-unoise2.log'
if os.path.isfile(log_name):
os.remove(log_name)
ufitslib.setupLogging(log_name)
FNULL = open(os.devnull, 'w')
cmd_args = " ".join(sys.argv) + '\n'
ufitslib.log.debug(cmd_args)
print "-------------------------------------------------------"
#initialize script, log system info and usearch version
ufitslib.SystemInfo()
#Do a version check
usearch = args.usearch
ufitslib.versionDependencyChecks(usearch)
#make tmp folder
tmp = args.out + '_tmp'
if not os.path.exists(tmp):
os.makedirs(tmp)